To burn a bootloader, you need an AVR In System Programmer, such as
http://www.mdfly.com/index.php?main_page=product_info&cPath=5&products_id=415
Connect it to the ICSP header, select Tools:Programmer:select the bootloader
Then Tools: Burn Bootloader.
You blank chip must either be in a board, or wired up like an Uno: 16 MHz crystal, 22 pf caps from crystal pins to gnd, 10K pullup resistor from reset to +5, 100nF caps on VCC, AVCC to Gnd. Programmer then connects to +5, Gnd, and Reset, SCK, MOSI, MISO pins.
I think I had to add 2 lines to programmers.txt to make it show up in the list, and add the drivers for it when it was connected to the PC the first time.